Find research datasets worth reusing

Codes and datasets for: Quantifying the impact of SARS-CoV-2 temporal vaccination trends and disparities on disease control

Codes and datasets to reproduce the main figures of the article titled: "Quantifying the impact of SARS-CoV-2 temporal vaccination trends and disparities on disease control".

The appendix for evaluating the impact of large-scale nucleic acid testing and home quarantine on COVID-19 prevention and control: a dynamic modeling approach

Appendix I: The program of evaluating the impact of large-scale nucleic acid testing and home quarantine on COVID-19 prevention and control: a dynamic modeling approach Appendix II: The sensitivity analysis of evaluating the impact of large-scale nucleic acid testing and home quarantine on COVID-19 prevention and control: a dynamic modeling approach

opencc-by-4.0Dec 2022View details →

Genetic impacts on DNA methylation help elucidate regulatory genomic processes

Background: Pinpointing genetic impacts on DNA methylation can improve our understanding of pathways that underlie gene regulation and disease risk. Results: We report heritability and methylation quantitative trait locus (meQTL) analysis at 724,499 CpGs profiled with the Illumina Infinium MethylationEPIC array in 2,358 blood samples from three UK cohorts. Methylation levels at 34.2% of CpGs are affected by SNPs, and 98% of effects are cis-acting or within 1 Mbp of the tested CpG. Our results are consistent with meQTL analyses based on the former Illumina Infinium HumanMethylation450 array. Both SNPs and CpGs with meQTLs are overrepresented in enhancers, which have improved coverage on this platform compared to previous approaches. Co-localisation analyses across genetic effects on DNA methylation and 56 human traits identify 1,520 co-localisations across 1,325 unique CpGs and 34 phenotypes, including in disease-relevant genes, such as USP1 and DOCK7 (total cholesterol levels), and ICOSLG (inflammatory bowel disease). Enrichment analysis of meQTLs and integration with expression QTLs give insights into mechanisms underlying cis-meQTLs, (e.g. through disruption of transcription factor binding sites for CTCF and SMC3), and trans-meQTLs (e.g. through regulating the expression of ACD and SENP7 which can modulate DNA methylation at distal sites). Conclusions: Our findings improve the characterisation of the mechanisms underlying DNA methylation variability and are informative for prioritisation of GWAS variants for functional follow-ups. The MeQTL EPIC Database and viewer are available online at <a href="https://epicmeqtl.kcl.ac.uk/">https://epicmeqtl.kcl.ac.uk/</a>.

Climate change impact on vernacular and archaeological cultural heritage building materials in Europe and Latin America

The analysis and interpretation of past climate data and simulations of climate models for future periods will allow us to study the impacts of climate change on cultural Heritage. The H2020 SCORE project (Sustainable COnservation and REstoration of built cultural heritage – 2020-2024) centres on two types of cultural heritage that differ by their geographical location and therefore their climatic conditions, as are vernacular cultural heritage in Europe (6 sites in Denmark, France, Italy and Spain) and archaeological sites in Latin America (2 sites in Mexico). All the cases study share a fundamental similarity in terms of the use of materials and construction techniques. One objective of the project is to quantify the impacts of continuous climate and pollution changes on building materials of cultural heritage under future IPCC socioeconomic scenarios with high and low mitigation measures at years 2030, 2050 and 2070, using peer-reviewed dose-response equations. We also focus on the degradation effects due to extreme events (heatwave, dry spells and extreme rainfall/flood) of each of the selected regions of our cases study. We apply these climatic conditions past and future) in different models, based on scientific literature, that allow estimate the weathering of the materials employed in the construction of cultural heritage buildings. Finally, we deliver preliminary results for a “cocktail of extreme events” based on the literature review and experiment in laboratory specifically designed to quantify the damages and degradation of building materials due to a realistic series of adverse climate and pollution events. We present here some results of future weathering (2081-2100) compared to near par (2001-2020) for different weathering process under the SSP5- RCP 8.5 scenario. The evolution of each process is different and it is different form one site to the other.

opennotspecifiedJun 2023View details →

FIGURE 1 in Palaeoentomology (2018-2022): A newcomer on the rise to high impact

FIGURE 1. The numbers of papers, pages, and citations in the first five years of Palaeoentomology. Citation data from Web of Science Core Collection™ (10 April 2023).

Aggressive interactions among white-tailed deer and their impact on the use of 4-poster devices for host-targeted tick control

Spreadsheet of data transcribed from images of deer and non-target wildlife with coded behaviors used in the manuscript "Aggressive interactions among white-tailed deer and their impact on the use of 4-poster devices for host-targeted tick control". Data involves cameras placed at three sites in Maryland 2016-2017.

Supplementary analysis 1 for Vitamin D status during adolescence and the impact of lifestyle changes – two years follow-up from the Fit Futures Study

Supplementary analysis 1: multiple regression model including BMI instead of physical activity.

opencc-by-4.0Nov 2022View details →

Do Design Rules Have an Impact on the Understandability of RESTful APIs? A Web-Based Experiment with API Descriptions

This repository contains materials of a controlled experiment with 105 participants that studied the impact of design rules on the understandability of RESTful APIs. The following materials are provided: <ul> <li>The data set (<code>results.csv</code>) with a description (<code>data-set-description.md</code>)</li> <li>The cleaning protocol (<code>data-cleaning-protocol.md</code>)</li> <li>The R analysis script (<code>analysis.R</code>)</li> <li>The two OpenAPI documents used as the foundation for the experiment <ul> <li>Adhering to the rules: <code>openapi-rules.yaml</code></li> <li>Violating the rules: <code>openapi-violations.yaml</code></li> </ul> </li> </ul>

A 3D printed plastic frame deeply impacts yeast cell growth

Solid State Fermentation (SSF) processes have been explored for yeast growth and protein and metabolites production. However, most of these processes lack standardization. In this work, we present a polylactic acid (PLA) 3D printed matrix that dramatically enhances yeast growth when embedded in liquid media compared to equivalent static cultures, and changes yeast expression patterns at the proteome level. Moreover, differences in sugar assimilation and ethanol production, as the main product of alcoholic fermentation, are observed. Our results suggest that these matrixes may be useful for a vast range of biotechnological applications based on yeast fermentation. Here we submit the proteomic data of this paper.

opencc-zeroJul 2023View details →

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Renewable energies and biodiversity: impact of ground-mounted solar photovoltaic sites on bat activity

<ol> <li>Renewable energy is growing at a rapid pace globally, but as yet there has been little research on the effects of ground-mounted solar photovoltaic (PV) developments on bats, many species of which are threatened or protected.</li> <li>We conducted a paired study at 19 ground-mounted solar PV developments in southwest England. We used static detectors to record bat echolocation calls from boundaries (i.e., hedgerows) and central locations (open areas) at fields with solar PV development, and simultaneously at matched sites without solar PV developments (control fields). We used generalized linear mixed-effect models to assess how solar PV developments and boundary habitat affected bat activity and species richness.</li> <li>The activity of six of eight species/species groups analysed was negatively affected by solar PV panels, suggesting that loss and/or fragmentation of foraging/commuting habitat is caused by ground-mounted solar PV panels. Pipistrellus pipistrellus and Nyctalus spp. activity was lower at solar PV sites regardless of the habitat type considered. Negative impacts of solar PV panels at field boundaries were apparent for the activity of Myotis spp. and Eptesicus serotinus, and in open fields for Pipistrellus pygmaeus and Plecotus spp.</li> <li>Bat species richness was greater along field boundaries compared with open fields, but there was no effect of solar PV panels on species richness.</li> <li> Policy Implications: Ground-mounted solar PV developments have a significant negative effect on bat activity, and should be considered in appropriate planning legislation and policy. Solar PV developments should be screened in Environmental Impact Assessments for ecological impacts, and appropriate mitigation (e.g., maintaining boundaries, planting vegetation to network with surrounding foraging habitat) and monitoring should be implemented to highlight potential negative effects.</li> </ol>

opencc-by-4.0Nov 2022View details →

MeCareNWL - baseline data concerning the psychosocial and occupational impact of COVID-19 among NHS and social care staff in NW London

Online survey data collected at baseline for participants enrolled in the MeCareNWL study - see <a href="https://arc-nwl.nihr.ac.uk/research/covid-19/london-wide-covid-19-research/mecarenwl">MeCareNWL (nihr.ac.uk)</a>. Data extracted from the Qualtrics database on 13 July 2021.  Some additional post-processing to satisfy anonymisation requirements. A pdf copy of the survey and the completed STROBE reporting checklist are also included.

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Urbanisation impacts plumage colouration in a songbird across Europe: evidence from a correlational, experimental, and meta-analytical approach

Urbanisation is increasing rapidly across the globe, transforming landscapes, presenting organisms with novel challenges, shaping phenotypes, and impacting fitness. Urban individuals are claimed to have duller tones in carotenoid-based traits, the so-called ″urban dullness″ phenomenon. However, at the intra-specific level, this generalisation is surprisingly inconsistent and often based on examples from few populations or a limited geographic area. Here, combining correlational, experimental, and meta-analytical results from a common songbird, the great tit (Parus major), we investigated carotenoid-based plumage coloration in urban and forest populations across Europe. We find that, as predicted, urban individuals are paler than forest individuals, although there are large population-specific differences in the magnitude of the urban-forest contrast in colouration. Our meta-analysis indicates a non-significant effect of environmental pollution on carotenoid-based plumage for the species, suggesting that the observed differences across urban populations are not only driven by pollution. Finally, using one region as an example (Malmö, Sweden), we reveal population-specific processes behind plumage colouration differences, which are likely the result of variation in the spatial and temporal distribution of carotenoid-rich resources in anthropogenic environments. Our results provide convincing evidence for consistency on the "urban dullness" phenomenon but highlight that its magnitude depends on local urban characteristics.

opencc-zeroJul 2023View details →

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Data from: Warming-induced functional shifts in the decomposer community interact with plant community compositional shifts to impact litter decomposition

<ol> <li>Climate warming is altering plant and soil microbial communities, with important implications for ecosystem processes like litter decomposition. As warming alters plant community composition, quality of litter will change. Further, shifts in microbial community activity and/or composition will alter microbial function. However, it is not yet completely understood how these shifts will interact to drive decomposition.</li> <li>We explored how changes in plant and microbial communities interact to influence litter decomposition using a 15-year-old grassland warming experiment. Previous studies within this system have shown that warming shifted the microbial community in ways that accelerate litter decomposition while simultaneously shifting the plant community in ways that may slow decomposition. Specifically, warming increased abundance of Sorghastrum nutans, while decreasing abundance of the previously dominant Schizachyrium scoparium. Using a series of lab-based microcosm experiments, we examined the rate at which eight common grasses and, separately, varying abundances of S. nutans and S. scoparium decomposed. Using litter and soil from the warming experiment, we then incubated soils from warmed or control plots with different abundances of S. nutans and S. scoparium in a reciprocal design.</li> <li>We found S. nutans to be the slowest-decomposing grass in our system. Further, decomposition slowed as S. nutans increased and S. scoparium decreased. When examining the interaction of plant and microbial communities, decomposition was generally greater early in our experiment as the relative abundance of S. scoparium increased. However, soil microbial community origin and litter composition interacted significantly. Specifically, decomposition increased with greater relative abundance of S. scoparium on soils derived from control plots, while litter composition did not shape rates of decomposition on soils from warmed plots. The influence of litter species on decomposition waned in the later stages of the experiment when decomposition was driven by microbial community origin.</li> <li>These results suggest that warming-induced changes in microbial community function may interact with changes in plant litter composition to mitigate the impacts of warming on rates of decomposition. This emphasizes the importance of considering concurrent warming-induced changes in both plant and microbial communities on ecosystem processes like decomposition.</li> </ol>

opencc-zeroJul 2023View details →

No impact of cyantraniliprole on the hibernation success of bumble bees (Bombus terrestris audax) in a soil-mediated laboratory exposure study

Dataset associated with the paper: "no evidence that soil-mediated exposure to cyantraniliprole alters the overwintering success of bumblebees (Bombus terrestris ssp. audax)"

Configuration optimization with limited functional impact

This dataset contains the validation and replication data for the paper Configuration Optimization with limited functional impact.

The impact of energy releasing B-vitamin intake on indices of obesity and cardiac function: a cross-sectional study

Supplementary file 1

Impacts of extratropical North Pacific on boreal summer Arctic circulation

Codes for the results shown in a manuscript titled "Impacts of North Pacific on boreal summer Arctic circulation" which is to be published at Atmospheric and Oceanic Science Letters.

The impact of energy releasing B-vitamin intake on indices of obesity and cardiac function: a cross-sectional study

Consent form

The impact of energy releasing B-vitamin intake on indices of obesity and cardiac function: a cross-sectional study

Study Questionnaire

Ca isotope data and codes for "Moon's high-energy giant-impact origin and differentiation timeline inferred from Ca and Mg stable isotopes"

Ca isotope data for "Moon’s high-energy giant-impact origin and differentiation timeline inferred from Ca and Mg stable isotopes" published in Communications Earth & Environment (2023)